Former University of San Diego standout quarterback Josh Johnson will reunite with former USD head coach Jim Harbaugh after signing a two-year deal with the NFL’s San Francisco 49ers on Thursday.

Johnson, who played at USD under Harbaugh for three seasons (2004-06), and his final year (2007) under current head coach Ron Caragher, is also returning to the Bay Area where he grew up in Oakland.

Johnson, 25, was a fifth-round pick in the 2008 draft and has spent the past four seasons with the Tampa Bay Buccaneers. During that time he earned five starts and has completed 96-of-177 passes with five touchdowns and 10 interceptions.

Stated Niners general manager Trent Baalke, “Josh is a promising young player that has experience in our offensive system. He is a skilled athlete with good arm talent. He has shown promise in limited action, both as a backup and starter at the NFL level. We are pleased to add him to our team.”

Johnson, 6-foot-3 and 205 pounds, is expected to back-up Alex Smith and presumably compete with Colin Kaepernick, a second-round pick in the 2010 draft. The 49ers also have a fourth quarterback on their roster, Scott Tolzien, who is an undrafted free agent that will be entering his second season.

When Harbaugh was first hired by USD back in 2003, the first player he recruited to USD was Johnson, who prepped at Oakland Tech and as a senior was just 5-9, 160 pounds.

When Johnson left USD four years later, he was the all-time NCAA pass efficiency leader and a Walter Payton Award Watch finalist. For his four-year career he completed 724-of-1,065 passes (.680) for 9,699 yards and 113 touchdowns against just 15 interceptions. Additionally, he rushed for 1,864 yards and 19 touchdowns, finishing his career with 11,563 yards of total offense. He was 30-4 as a starter over his final three seasons with the Toreros. During his final season at USD in 2007, Johnson completed 206-of-301 passes (.684) for 2,988 yards and 43 touchdowns and just one interception.